[English] 日本語
Yorodumi
- EMDB-1609: VP6-VP7 complex structure from VP7 recoated rotavirus DLP -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1609
TitleVP6-VP7 complex structure from VP7 recoated rotavirus DLP
Keywordsrotavirus / capsid / VP7 / VP6 / VP2
SampleVP7 recoated rotavirus DLP
SourceBos taurus / mammal / Bovine / ウシ /
Map dataT13 non-icosahedral local averaging
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsChen JZ / Settembre EC / Aoki ST / Zhang X / Bellamy AR / Dormitzer PR / Harrison SC / Grigorieff N
CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 10644-10648

Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 10644-10648 Yorodumi Papers
Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.
James Z Chen / Ethan C Settembre / Scott T Aoki / Xing Zhang / A Richard Bellamy / Philip R Dormitzer / Stephen C Harrison / Nikolaus Grigorieff

Validation ReportPDB-ID: 3gzt

SummaryFull report
PDB-ID: 3gzu

SummaryFull report
About validation report
DateDeposition: Mar 25, 2009 / Header (metadata) release: Apr 8, 2009 / Map release: May 18, 2009 / Last update: Mar 9, 2012

-
Structure visualization

Movie
  • Colored surface
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1609.map.gz (map file in CCP4 format, 3268 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
108 pix
1.23 Å/pix.
= 133.164 Å
88 pix
1.23 Å/pix.
= 108.504 Å
88 pix
1.23 Å/pix.
= 108.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.233 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-4.63558674 - 6.8486414
Average (Standard dev.)-1E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions8888108
Origin000
Limit8787107
Spacing8888108
CellA: 108.504005 Å / B: 108.504005 Å / C: 133.164 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2331.2331.233
M x/y/z8888108
origin x/y/z0.0000.0000.000
length x/y/z108.504108.504133.164
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8888108
D min/max/mean-4.6366.849-0.000

-
Supplemental data

-
Sample components

-
Entire VP7 recoated rotavirus DLP

EntireName: VP7 recoated rotavirus DLP / Number of components: 3 / Oligomeric State: icosahedral virus capsid
MassTheoretical: 60 MDa / Experimental: 60 MDa / Measured by: Sum of all components

-
Component #1: protein, VP7

ProteinName: VP7 / a.k.a: VP7 / Oligomeric Details: Trimer / Number of Copies: 780 / Recombinant expression: No
MassTheoretical: 37.4 kDa / Experimental: 37.4 kDa
SourceSpecies: Bos taurus / mammal / Bovine / ウシ /

-
Component #2: protein, VP6

ProteinName: VP6 / a.k.a: VP6 / Oligomeric Details: Trimer / Recombinant expression: No / Number of Copies: 780
MassTheoretical: 44.8 kDa / Experimental: 44.8 kDa
SourceSpecies: Bos taurus / mammal / Bovine / ウシ /

-
Component #3: protein, VP2

ProteinName: VP2 / a.k.a: VP2 / Oligomeric Details: Dimer / Recombinant expression: No / Number of Copies: 120
MassTheoretical: 94 kDa / Experimental: 94 kDa
SourceSpecies: Bos taurus / mammal / Bovine / ウシ /

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / Buffer solution: 20mM Tris-HCl, 50mM NaCl, 2mM CaCl2 / pH: 8
Support filmC-flat grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 90 % / Method: Blot for 3 seconds before plunging / Details: Vitrification instrument: manual plunger

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Dec 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 58168 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 90 - 90 K)
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 148 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3780
Details: The particles were selected using SIGNATURE, the density map was reconstructed and refined using FREALIGN.
3D reconstructionAlgorithm: Projection matching / Software: FREALIGN / CTF correction: Individual particle / Resolution: 4.2 Å / Resolution method: FSC 0.143

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more